Yingjin Yuan has designed a yeast artificial chromosome, and stored two pictures and a video in it.Credit: Tianjin University
Amid rapid digitalization, humans generate millions of gigabytes of data each day. Global data volume will reach about 180 zettabytes (where 1 ZB is 1012 GB) by 2025. Finding economically viable storage solutions for such a massive amount of data is a major challenge.
To tackle the conundrum, Yingjin Yuan, a professor of biochemical engineering at Tianjin University, turned to deoxyribonucleic acid (DNA) and has designed yeast artificial chromosomes as a potential solution.
“DNA has evolved to store massive quantities of information at very high density, and it’s remarkably stable, too. The largest human chromosome carries up to 250 million base pairs of DNA. If data could be stored on every base pair, all the data in the world could theoretically fit in a coffee mug,” says Yuan.
Yeast, a single-cell microorganism, typically has 16 chromosomes. Using a synthetic biological technique, Yuan’s team has designed and synthesized an extra yeast chromosome in a live cell. They employed a clever error correction encoding scheme using sparsified low-density parity check (LDPC) codes ― a method of transmitting a message over a noisy transmission channel, and pseudo random sequences. Then the digital files were encoded into codewords, and further transcoded into synthetic DNA chunks. Finally, these DNA chunks were assembled into an artificial chromosome.
With this approach, the artificial chromosome is designed to carry 254 kilobases (1kb = 1,000 bases) of DNA. The team has successfully stored two pictures and a video in it, and the encoded data occupies more than 95% of the sequence1. “Our work broke through the current DNA data storage limit of only a few thousand bases per genome, “ says Yuan.
Self-replicable
The data-carrying chromosome can be replicated stably in yeast for multiple retrievals. With DNA self-replicating in the cell body, digital information can be amplified exponentially before the data is read out with a nanopore sequencer.
Yuan’s team demonstrated the stability of this DNA storage mode by transmitting the data-carrying chromosome to the 100th generation. The transcription of the chromosome is active while no new protein was translated, and the yeast growth was not significantly affected2.
“DNA digital data storage has the advantage of high storage density, long storage time and low energy consumption,” says Yuan. “The DNA storage density potential is 10 million times that of traditional media such as hard disks and tapes. Its storage could last over 1,000 years at room temperature, and it could reduce the energy consumption by 1,000 times compared to today’s data centres.”
However, DNA storage currently faces many challenges, such as high cost for DNA synthesis, and slow read and write speed. Several key technological breakthroughs are essential, including designing codes that adapt to the DNA medium, on what type of DNA medium, and how to read data better and faster.
Yuan’s team is looking to solve the challenges of genome synthesis, such as comprehensive design of microbial genome, high-throughput DNA synthesis, and efficient chromosome assembly. “We will continue our research to achieve ultra-low-cost synthesis of large-scale DNA for green data storage.”
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